NIFD_CLOPA
ID NIFD_CLOPA Reviewed; 534 AA.
AC P00467;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Nitrogenase molybdenum-iron protein alpha chain;
DE EC=1.18.6.1;
DE AltName: Full=Dinitrogenase;
DE AltName: Full=Nitrogenase component I;
GN Name=nifD;
OS Clostridium pasteurianum.
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae;
OC Clostridium.
OX NCBI_TaxID=1501;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3473447; DOI=10.1093/nar/15.9.3935;
RA Wang S.-Z., Chen J.-S., Johnson J.L.;
RT "Nucleotide and deduced amino acid sequences of nifD encoding the alpha-
RT subunit of nitrogenase MoFe protein of Clostridium pasteurianum.";
RL Nucleic Acids Res. 15:3935-3935(1987).
RN [2]
RP PROTEIN SEQUENCE OF 2-180.
RX PubMed=7026551; DOI=10.1093/oxfordjournals.jbchem.a133466;
RA Hase T., Nakano T., Matsubara H., Zumft W.G.;
RT "Correspondence of the larger subunit of the MoFe-protein in clostridial
RT nitrogenase to the nif D gene products of other N2-fixing organisms.";
RL J. Biochem. 90:295-298(1981).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-167.
RX PubMed=3457003; DOI=10.1128/jb.166.1.162-172.1986;
RA Chen K.C.K., Chen J.-S., Johnson J.L.;
RT "Structural features of multiple nifH-like sequences and very biased codon
RT usage in nitrogenase genes of Clostridium pasteurianum.";
RL J. Bacteriol. 166:162-172(1986).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 526-534.
RX PubMed=2840948; DOI=10.1021/bi00408a021;
RA Wang S.-Z., Chen J.-S., Johnson J.L.;
RT "Distinct structural features of the alpha and beta subunits of nitrogenase
RT molybdenum-iron protein of Clostridium pasteurianum: an analysis of amino
RT acid sequences.";
RL Biochemistry 27:2800-2810(1988).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH 8FE-7S CLUSTER AND
RP 7FE-MO-9S-C-HOMOCITRYL CLUSTER, SUBUNIT, AND COFACTOR.
RX PubMed=8393705; DOI=10.1021/bi00079a006;
RA Kim J., Woo D., Rees D.C.;
RT "X-ray crystal structure of the nitrogenase molybdenum-iron protein from
RT Clostridium pasteurianum at 3.0-A resolution.";
RL Biochemistry 32:7104-7115(1993).
CC -!- FUNCTION: This molybdenum-iron protein is part of the nitrogenase
CC complex that catalyzes the key enzymatic reactions in nitrogen
CC fixation.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=16 ATP + 16 H2O + N2 + 8 reduced [2Fe-2S]-[ferredoxin] = 16
CC ADP + 6 H(+) + H2 + 2 NH4(+) + 8 oxidized [2Fe-2S]-[ferredoxin] + 16
CC phosphate; Xref=Rhea:RHEA:21448, Rhea:RHEA-COMP:10000, Rhea:RHEA-
CC COMP:10001, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17997,
CC ChEBI:CHEBI:18276, ChEBI:CHEBI:28938, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:456216; EC=1.18.6.1;
CC -!- COFACTOR:
CC Name=[8Fe-7S] cluster; Xref=ChEBI:CHEBI:21143;
CC Evidence={ECO:0000269|PubMed:8393705};
CC Note=Binds 1 [8Fe-7S] cluster per heterodimer.
CC {ECO:0000269|PubMed:8393705};
CC -!- COFACTOR:
CC Name=[7Fe-Mo-9S-C-homocitryl] cluster; Xref=ChEBI:CHEBI:30409;
CC Evidence={ECO:0000269|PubMed:8393705};
CC Note=Binds 1 [7Fe-Mo-9S-C-homocitryl] cluster per subunit.
CC {ECO:0000269|PubMed:8393705};
CC -!- SUBUNIT: Tetramer of two alpha and two beta chains. Forms complex with
CC the iron protein (nitrogenase component 2).
CC {ECO:0000269|PubMed:8393705}.
CC -!- SIMILARITY: Belongs to the NifD/NifK/NifE/NifN family. {ECO:0000305}.
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DR EMBL; AY603957; AAA83531.2; -; Genomic_DNA.
DR PIR; S07389; NICLMA.
DR RefSeq; WP_003447876.1; NZ_LFYL01000003.1.
DR PDB; 1MIO; X-ray; 3.00 A; A/C=2-534.
DR PDB; 4WES; X-ray; 1.08 A; A/C=1-534.
DR PDB; 4WN9; X-ray; 1.90 A; A/C=3-520.
DR PDB; 5VPW; X-ray; 1.85 A; A/C=1-520.
DR PDB; 5VQ3; X-ray; 1.72 A; A/C=1-520.
DR PDBsum; 1MIO; -.
DR PDBsum; 4WES; -.
DR PDBsum; 4WN9; -.
DR PDBsum; 5VPW; -.
DR PDBsum; 5VQ3; -.
DR AlphaFoldDB; P00467; -.
DR SMR; P00467; -.
DR BioCyc; MetaCyc:NIFDCP-MON; -.
DR BRENDA; 1.18.6.1; 1502.
DR EvolutionaryTrace; P00467; -.
DR GO; GO:0016612; C:molybdenum-iron nitrogenase complex; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0018697; F:carbonyl sulfide nitrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016163; F:nitrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-KW.
DR InterPro; IPR000510; Nase/OxRdtase_comp1.
DR InterPro; IPR010143; Nase_comp1_asu.
DR InterPro; IPR000318; Nase_comp1_CS.
DR InterPro; IPR005972; Nase_Mo-Fe_asu.
DR PANTHER; PTHR43457; PTHR43457; 1.
DR Pfam; PF00148; Oxidored_nitro; 1.
DR TIGRFAMs; TIGR01862; N2-ase-Ialpha; 1.
DR TIGRFAMs; TIGR01282; nifD; 1.
DR PROSITE; PS00699; NITROGENASE_1_1; 1.
DR PROSITE; PS00090; NITROGENASE_1_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Direct protein sequencing; Iron; Iron-sulfur;
KW Metal-binding; Molybdenum; Nitrogen fixation; Nucleotide-binding;
KW Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7026551"
FT CHAIN 2..534
FT /note="Nitrogenase molybdenum-iron protein alpha chain"
FT /id="PRO_0000153064"
FT BINDING 53
FT /ligand="[8Fe-7S] cluster"
FT /ligand_id="ChEBI:CHEBI:21143"
FT /ligand_note="ligand shared with beta chain"
FT BINDING 79
FT /ligand="[8Fe-7S] cluster"
FT /ligand_id="ChEBI:CHEBI:21143"
FT /ligand_note="ligand shared with beta chain"
FT BINDING 145
FT /ligand="[8Fe-7S] cluster"
FT /ligand_id="ChEBI:CHEBI:21143"
FT /ligand_note="ligand shared with beta chain"
FT BINDING 262
FT /ligand="[7Fe-Mo-9S-C-homocitryl] cluster"
FT /ligand_id="ChEBI:CHEBI:30409"
FT BINDING 482
FT /ligand="[7Fe-Mo-9S-C-homocitryl] cluster"
FT /ligand_id="ChEBI:CHEBI:30409"
FT CONFLICT 42
FT /note="R -> K (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 95
FT /note="N -> D (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 5..10
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 15..22
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:4WN9"
FT HELIX 54..58
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 59..63
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 69..76
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 77..81
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 84..87
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 94..96
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:1MIO"
FT HELIX 112..117
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 120..134
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 146..149
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 154..165
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 182..196
FT /evidence="ECO:0007829|PDB:4WES"
FT TURN 197..199
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 221..232
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 235..241
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 246..250
FT /evidence="ECO:0007829|PDB:4WES"
FT TURN 251..253
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 256..262
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 263..277
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 281..283
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 289..303
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 306..334
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 338..346
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 347..350
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 352..357
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 361..369
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 372..376
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 378..383
FT /evidence="ECO:0007829|PDB:4WES"
FT TURN 388..392
FT /evidence="ECO:0007829|PDB:4WES"
FT TURN 402..404
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 411..419
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 430..433
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 439..441
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 446..456
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 459..463
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 465..473
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 480..483
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 492..507
FT /evidence="ECO:0007829|PDB:4WES"
FT HELIX 510..513
FT /evidence="ECO:0007829|PDB:4WES"
FT STRAND 518..524
FT /evidence="ECO:0007829|PDB:1MIO"
SQ SEQUENCE 534 AA; 59126 MW; D8E8B73D144B6673 CRC64;
MSENLKDEIL EKYIPKTKKT RSGHIVIKTE ETPNPEIVAN TRTVPGIITA RGCAYAGCKG
VVMGPIKDMV HITHGPIGCS FYTWGGRRFK SKPENGTGLN FNEYVFSTDM QESDIVFGGV
NKLKDAIHEA YEMFHPAAIG VYATCPVGLI GDDILAVAAT ASKEIGIPVH AFSCEGYKGV
SQSAGHHIAN NTVMTDIIGK GNKEQKKYSI NVLGEYNIGG DAWEMDRVLE KIGYHVNATL
TGDATYEKVQ NADKADLNLV QCHRSINYIA EMMETKYGIP WIKCNFIGVD GIVETLRDMA
KCFDDPELTK RTEEVIAEEI AAIQDDLDYF KEKLQGKTAC LYVGGSRSHT YMNMLKSFGV
DSLVAGFEFA HRDDYEGREV IPTIKIDADS KNIPEITVTP DEQKYRVVIP EDKVEELKKA
GVPLSSYGGM MKEMHDGTIL IDDMNHHDME VVLEKLKPDM FFAGIKEKFV IQKGGVLSKQ
LHSYDYNGPY AGFRGVVNFG HELVNGIYTP AWKMITPPWK KASSESKVVV GGEA
